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Variational bayesian method of estimating variance components.
Anim Sci J. 2016 Jul; 87(7):863-72.AS

Abstract

We developed a Bayesian analysis approach by using a variational inference method, a so-called variational Bayesian method, to determine the posterior distributions of variance components. This variational Bayesian method and an alternative Bayesian method using Gibbs sampling were compared in estimating genetic and residual variance components from both simulated data and publically available real pig data. In the simulated data set, we observed strong bias toward overestimation of genetic variance for the variational Bayesian method in the case of low heritability and low population size, and less bias was detected with larger population sizes in both methods examined. The differences in the estimates of variance components between the variational Bayesian and the Gibbs sampling were not found in the real pig data. However, the posterior distributions of the variance components obtained with the variational Bayesian method had shorter tails than those obtained with the Gibbs sampling. Consequently, the posterior standard deviations of the genetic and residual variances of the variational Bayesian method were lower than those of the method using Gibbs sampling. The computing time required was much shorter with the variational Bayesian method than with the method using Gibbs sampling.

Authors+Show Affiliations

Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.Agroinformatics Division, National Agriculture and Food Research Organization, Agricultural Research Center, Tsukuba, Ibaraki, Japan.Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

26877207

Citation

Arakawa, Aisaku, et al. "Variational Bayesian Method of Estimating Variance Components." Animal Science Journal = Nihon Chikusan Gakkaiho, vol. 87, no. 7, 2016, pp. 863-72.
Arakawa A, Taniguchi M, Hayashi T, et al. Variational bayesian method of estimating variance components. Anim Sci J. 2016;87(7):863-72.
Arakawa, A., Taniguchi, M., Hayashi, T., & Mikawa, S. (2016). Variational bayesian method of estimating variance components. Animal Science Journal = Nihon Chikusan Gakkaiho, 87(7), 863-72. https://doi.org/10.1111/asj.12514
Arakawa A, et al. Variational Bayesian Method of Estimating Variance Components. Anim Sci J. 2016;87(7):863-72. PubMed PMID: 26877207.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Variational bayesian method of estimating variance components. AU - Arakawa,Aisaku, AU - Taniguchi,Masaaki, AU - Hayashi,Takeshi, AU - Mikawa,Satoshi, Y1 - 2016/02/15/ PY - 2015/04/20/received PY - 2015/06/02/revised PY - 2015/06/18/accepted PY - 2016/2/16/entrez PY - 2016/2/16/pubmed PY - 2017/3/17/medline KW - Gibbs sampling KW - linear mixed model KW - spectral decomposition SP - 863 EP - 72 JF - Animal science journal = Nihon chikusan Gakkaiho JO - Anim Sci J VL - 87 IS - 7 N2 - We developed a Bayesian analysis approach by using a variational inference method, a so-called variational Bayesian method, to determine the posterior distributions of variance components. This variational Bayesian method and an alternative Bayesian method using Gibbs sampling were compared in estimating genetic and residual variance components from both simulated data and publically available real pig data. In the simulated data set, we observed strong bias toward overestimation of genetic variance for the variational Bayesian method in the case of low heritability and low population size, and less bias was detected with larger population sizes in both methods examined. The differences in the estimates of variance components between the variational Bayesian and the Gibbs sampling were not found in the real pig data. However, the posterior distributions of the variance components obtained with the variational Bayesian method had shorter tails than those obtained with the Gibbs sampling. Consequently, the posterior standard deviations of the genetic and residual variances of the variational Bayesian method were lower than those of the method using Gibbs sampling. The computing time required was much shorter with the variational Bayesian method than with the method using Gibbs sampling. SN - 1740-0929 UR - https://www.unboundmedicine.com/medline/citation/26877207/Variational_bayesian_method_of_estimating_variance_components_ L2 - https://doi.org/10.1111/asj.12514 DB - PRIME DP - Unbound Medicine ER -